An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

Cartney, Ann Mc; Mahmoud, Medhat; Jochum, Michael D.; Agustinho, Daniel Paiva; Zorman, Barry; Khleifat, Ahmad Al; Dabbaghie, Fawaz; Kesharwani, Rupesh K.; Smolka, Moritz; Dawood, Moez; Albin, Dreycey; Aliyev, Elbay; Almabrazi, Hakeem; Arslan, Ahmed; Balaji, Advait; Behera, Sairam; Billingsley, Kimberley; Cameron, Daniel; Daw, Joyjit; Dawson, Eric T.; Coster, Wouter De; Du, Haowei; Dunn, Christopher; Esteban, Rocio; Jolly, Angad; Kalra, Divya; Liao, Chunxiao; Liu, Yunxi; Lu, Tsung-Yu; Havrilla, James M; Khayat, Michael M.; Marin, Maximillian G.; Monlong, Jean; Price, Stephen; Gener, Alejandro Rafael; Ren, Jimin; Sagayaradj, Sagayamary; Sapoval, Nicolae; Sinner, Claude; Soto, Daniela C.; Söylev, Arda; Subramaniyan, Arun; Syed, Najeeb; Tadimeti, Neha; Tater, Pamella; Vats, Pankaj; Vaughn, Justin N.; Walker, Kimberly; Wang, Gaojianyong; Zeng, Qiandong; Zhang, Shangzhe; Zhao, Tingting; Kille, Bryce; Biederstedt, Evan; Chaisson, Mark; English, Adam C.; Kronenberg, Zev; Treangen, Todd J.; Hefferon, Timothy; Chin, Chen-Shan; Busby, Ben; Sedlazeck, Fritz J.

doi:10.12688/f1000research.51477.2

Cited by 3 publications

(2 citation statements)

References 71 publications

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“…Hackathons have recently become popular in the health and biology domain, where the outcomes have focused on a variety of research disciplines and challenges. Some hackathons focus on the development of useful tools, such as the event hosted by DNAnexus and the Baylor College of Medicine in 2020, where participants created novel tools for structural variation and SARS-CoV-2 research 3 . Others focus on reaching a solution or creative idea to a research question through competition, such as the events using data from The Alzheimer’s Disease Neuroimaging Initiative (ADNI), where teams competed to predict mild cognitive impairment (MCI) conversion to Alzheimer’s Disease 4 .…”

Section: Introductionmentioning

confidence: 99%

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Leonard

Murtadha²,

Martínez-Carrasco³

et al. 2023

npj Parkinsons Dis.

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Open science and collaboration are necessary to facilitate the advancement of Parkinson’s disease (PD) research. Hackathons are collaborative events that bring together people with different skill sets and backgrounds to generate resources and creative solutions to problems. These events can be used as training and networking opportunities, thus we coordinated a virtual 3-day hackathon event, during which 49 early-career scientists from 12 countries built tools and pipelines with a focus on PD. Resources were created with the goal of helping scientists accelerate their own research by having access to the necessary code and tools. Each team was allocated one of nine different projects, each with a different goal. These included developing post-genome-wide association studies (GWAS) analysis pipelines, downstream analysis of genetic variation pipelines, and various visualization tools. Hackathons are a valuable approach to inspire creative thinking, supplement training in data science, and foster collaborative scientific relationships, which are foundational practices for early-career researchers. The resources generated can be used to accelerate research on the genetics of PD.

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Section: Introductionmentioning

confidence: 99%

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Leonard

Murtadha²,

Martínez-Carrasco³

et al. 2023

npj Parkinsons Dis.

View full text Add to dashboard Cite

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“…Furthermore, although we have assessed reported ALS-associated rare missense and loss of function variants in linkage disequilibrium with the structural variants, we cannot exclude the possibility that the differential risk and phenotypes observed could be modulated by small common single-nucleotide variants or indels in linkage disequilibrium with the structural variants. Using GeneVar SV data browser 43 , the estimated frequency of VCP inversion is 0.0005 and ERBB4 insertion 0.82. However, allele frequencies tend to vary across human populations, and different SV callers may give varying results between datasets.…”

Section: Discussionmentioning

confidence: 99%

Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis

et al. 2022

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There is a strong genetic contribution to Amyotrophic lateral sclerosis (ALS) risk, with heritability estimates of up to 60%. Both Mendelian and small effect variants have been identified, but in common with other conditions, such variants only explain a little of the heritability. Genomic structural variation might account for some of this otherwise unexplained heritability. We therefore investigated association between structural variation in a set of 25 ALS genes, and ALS risk and phenotype. As expected, the repeat expansion in the C9orf72 gene was identified as associated with ALS. Two other ALS-associated structural variants were identified: inversion in the VCP gene and insertion in the ERBB4 gene. All three variants were associated both with increased risk of ALS and specific phenotypic patterns of disease expression. More than 70% of people with respiratory onset ALS harboured ERBB4 insertion compared with 25% of the general population, suggesting respiratory onset ALS may be a distinct genetic subtype.

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The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

et al. 2022

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In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

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An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

Cited by 3 publications

References 71 publications

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

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